We will find a way
by PearlofAtlantis76
Summary: The events on this story all happen post "Enemy at the Gate" in a possible season 6, probably season 7, since they also follow the events created on "Atlantis Rising: - the Virtual series" the Virtual season 6 of Stargate Atlantis. So for a better understanding of my story, you might want to read "Atlantis Rising" first. :)
1. Chapter 1

**A/N:** I would like to say thank you to all the reviews given to my first story "Breakfast in Atlantis". Thank you so much for reading it. :) And just to clarify a few things, I know that **unfortunately** Elizabeth was _presumed _dead, that's right **_presumed_** dead on the show. I invite you all to please read this virtual continuation of Stargate Atlantis, a virtual season 6 called "Atlantis Rising", and you will see that my stories are kind of a follow up of that. :)

**Chapter 1**

**Atlantis conference room**

"Well that Ancient ship, the Travellers found on the Nibor system, sure seems to be worth a visit." Woolsey said.

"Yeah, definitely." Rodney begun. "But unfortunately with most of the science teams busy with the discoveries from M7L-787, there isn't a spare team available to go off-world right now." Rodney said sounding a little bit frustrated.

"Well, but according to the Travellers' intel, the ship seems to be mostly operational." Woolsey said. "The only reason they asked for our help was because they still need someone to initialise the remaining of the systems in order for the ship to be able to fly."

"You mean someone with the ATA gene". John spoke.

"That's right, Colonel." Woolsey replied. "There is also that strange lab on board they don't seem to be able to figure out what it is for."

"Hence the need for one of our science teams to be on board that ship as soon as possible." Rodney said.

"Definitely." Zelenka added.

"Well, in that case, if the science teams can't go there, why don't we bring the ship here instead?" John suggested.

"That thought had crossed my mind." Woolsey said. "But since we are short on personnel right now, the only pilot available is you, Colonel. But I will also need you to be here for the meeting with the Ascane. They are a military society and it would be better to introduce them to our military commander as soon as possible."

"Yeah, but they will only be here in two days." Rodney interrupted. "There will be more than enough time for Sheppard to get to the Ancient ship and bring it back here."

"So what are we waiting for?" Sheppard said. "I am ready to go."

"I was thinking that maybe Dr. Weir could go along with you, Colonel." Woolsey said. "She can begin the translation of the logs from the Ancient ship, while the ship is being brought here to Atlantis. I am guessing it will make things more expedite."

"Yes, because in that way, once the ship gets here, we can immediately start working on it, without having to wait for the linguistics department's team to go on board and do the translations". Zelenka said.

"There is only one problem." Rodney interrupted. "Elizabeth is off-world right now."

"She should be returning shortly." Woolsey said. "Meanwhile, Colonel, I guess you could go ahead and start preparing a Jumper."

Woolsey ended the meeting there and they all started leaving the conference room.

Suddenly, Chuck's announcement, of an off-world activation, is heard.

"Chuck" Woolsey said approaching the technician.

"It's Major Lorne's IDC, Sir." Chuck said.

A few moments later, the figures of Major Lorne, Elizabeth, Teyla, Kanaan and a few Marines, emerged from the shimmering blue puddle.

"How are the negotiations with the Pulgari?" Woolsey asked to the newly arrived group.

"Everything seems to be going well." Elizabeth answered, not sounding totally convinced. "At least according to the Pulgari's governor."

"I guess we can say that everything went well as far as the Pulgari goes." Teyla added.

"We all know how stubborn the Pulgari can be." This time it was Kanaan who spoke.

"So does Elizabeth." John said smirking.

"Well," Elizabeth said with a smile and a raised eyebrow, her gaze on John.

Woolsey cleared his throat.

"Colonel Sheppard will be departing shortly for the Nibor system, in the hopes of bringing the Ancient ship, found by the Travellers, to Atlantis." Woolsey started. "Dr. Weir, I know this is a bit sudden, but I would like you to go along with Colonel Sheppard.

"While I am bringing the Ancient ship here, you can begin the translations of the ship's logs, in order to make things more expedite. This way, when we get here, the science's teams will be able to go on board, with no further delays." John explained when he noticed Elizabeth's puzzling look.

"I have yet to download the report related with the Pulgari's negotiations, but after that, I am all yours." Elizabeth said, looking at John.

"Do not worry, Elizabeth. Kanaan and I can do that for you." Teyla offered with a smile.

"That's settled then." Woolsey said.

"When do we leave?" Elizabeth asked turning to John.

"In an hour." John replied. Turning then to Major Lorne, John ordered. "Major, I want you to assemble some teams, that will then accompany the science teams on board the Ancient ship.

"Yes, Sir." Major Lorne acknowledged.

TO BE CONTINUED…

***Thank you for reading.*** :) :D


	2. Chapter 2

**Jumper**

"You're awfully quiet." John noticed.

"Oh, I am sorry. I am trying to figure out how should I start the translations on this Ancient ship. I am assuming, it must be a research ship. Otherwise, there wouldn't be any point on having a lab on board." Elizabeth said looking from her tablet to John.

"I guess." John said. "But I am pretty sure you will have no problems with it."

John glanced over his shoulder, at the backpack full of books, Elizabeth had brought from Atlantis.

"Yeah…" Elizabeth said with a sheepish smile. John smiled back at her.

Someone trying to hail them interrupted them.

"This is Lt. Colonel John Sheppard." John said in reply to the hail.

"I am Kytoria from the Travelers." A woman said. Her image was now showing on the HUD.

"We came here because of the Ancient ship you…" John began.

"Of course, please follow my ship." Kytoria said interrupting curtly.

"Okay." John said drawling.

The connection between the two ships was terminated.

"That was interesting." Elizabeth said.

"Yeah…" John agreed.

Some moments later, John and Elizabeth found themselves alone aboard the Ancient ship. Kytoria returned to her own ship, after explaining that she has orders to escort the Ancient Ship back to Atlantis. By now, John had already activated some of the remaining systems the Travelers hadn't been able to initialise due to the lack of the ATA gene, so both he and Elizabeth were scrutinizing the outside of the mysterious lab. Inside, they came across some sort of interface.

"Let's see if I can initialise it." John said.

Elizabeth stepped back and John moved a little bit closer to the interface. It immediately activated, once John waved his hand over it. Elizabeth smiled and her eyes now seemed to be full of excitement. She then approached the interface, where a lot of data, in Ancient, could now be seen.

"Wow!" John said.

"Definitely wow!" Elizabeth agreed.

Elizabeth grabbed her tablet and tried to connect it to the interface.

"You know, this will probably take some time." Elizabeth spoke to John.

"Okay." John said drawling. "I should probably head to the bridge anyway, to see if we, or I, can make this ship fly us back to Atlantis."

"Have fun, captain." Elizabeth said smiling.

"See you in a bit." John said and started down the hall towards the bridge.

TO BE CONTINUED…

***Thank you for reading.*** :) :D


	3. Chapter 3

**A/N: **Thank you all, so much, for reading and for all the reviews. :) I am glad you are all enjoying this story, too. I sure hope this multi chapter story will meet your expectations.

John and Elizabeth alone, on an Ancient ship. ;) Easy mission, hmm…

Thank you so much to my friend Janus from betaying chapters 2 and 3. :)

* * *

The Ancient ship was now heading back through hyperspace towards Atlantis. John had set their course and engaged the autopilot, so now he was heading back towards the lab where he had left Elizabeth.

He should check on her, she had been awfully quiet. He picked up the pace, and his heart started beating a little bit faster. He had checked the Ancient ship with the biometric sensor and there was no one else but them aboard the ship. Then again, he should have learned by now that here in Pegasus, anything is possible.

John felt relieved when he saw that Elizabeth was still there, near the interface, unharmed, just very quiet. He approached her, doing his best not to startle her. She seemed to be in some kind of a trance.

"Elizabeth…?" John said.

"John!" Elizabeth replied, snapping from her deep trance.

"What's wrong?" John asked.

"Good, you're here. I was about to call you." Elizabeth said with a grin.

John could tell, just by looking at her and by the tone in her voice, that she had found something good.

"According to the database… this ship… was one of the ships the Ancients used to destroy Asuras. You know…the first time, when the Ancients decided to destroy all the Replicators, once they decided to end the experiment they were doing with them." Elizabeth explained.

"Really?!" John said in astonishment.

John opened his mouth and then closed it.

"Does that mean there's a chance that this ship might be infected with nanites?!" John said, freaking out a bit.

"No... At least I don't think so, because according to the database, this ship was used only for software development and upload, it doesn't have a nanite-generating machine. And besides, if it was infected, I think we'd know about it by now, or at least the Travelers would, since they found the ship and boarded it some time ago." Elizabeth explained.

"I dunno if that's good news, or not... might explain why they left no one of their people aboard..." John said.

"That would only make sense if they already knew about the contents of the database, and they lack both the knowledge of the Ancient language and the ATA gene." Elizabeth interrupted.

"I guess you're right, but after everything that happened with the Replicators, I'd suggest a bit of caution." John said.

John approached the interface, standing now beside Elizabeth. Sometimes John still couldn't believe they had actually found her. So much time had passed that no one, in Atlantis, ever would have expected to see the _real_ Elizabeth Weir being returned to them.

"And there's more." Elizabeth said. "According to the data, this lab was used to store the assimilation research archive."

"You mean…" John trailed off.

"Yes!" Elizabeth said with excitement.

"You think Rodney will be able to figure out something to help you?" John said smiling and looking at Elizabeth's excitement.

"John, do you know what this means?!" Elizabeth said grinning.

John could tell she hadn't really paid any attention to what he was trying to say.

"Yeah…" John said chuckling. Never the less, he was feeling a little bit incredulous about their discovery.

Elizabeth suddenly turned to him and putting her hands around his neck, she embraced him tightly. John, after a moment, embraced her back.

"John, I…" Elizabeth whispered close to John's ear.

"I know." John said smiling into her hair.

Elizabeth held him even tighter. John was feeling surprised by what she was doing. Since she had returned, she didn't seem to like much physical contact.

John suddenly pulled away from the hug, and gazed at her, his hands rising to her arms. He was now so close to her, he could feel her breath on his skin. Elizabeth looked up at him, searching his face for a clue to his thoughts right there, on that very moment. It didn't take her long to find the answer she was looking for. Because right there, on that instant, John's lips descended on her own.

TO BE CONTINUED…

***Thank you for reading.*** :) :D


End file.
